Variant report

Variant	rs2080177
Chromosome Location	chr4:15489722-15489723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15479756..15482166-chr4:15489455..15493787,3	MCF-7	breast:
2	chr4:15484757..15487117-chr4:15489258..15491846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048342	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1058412	0.81[CEU][hapmap]
rs11728800	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12500458	0.81[EUR][1000 genomes]
rs13131700	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1861048	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1861049	0.83[JPT][hapmap]
rs1861050	0.83[JPT][hapmap]
rs2080176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087622	0.83[EUR][1000 genomes]
rs34465372	0.85[EUR][1000 genomes]
rs4063953	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4140934	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698387	0.84[EUR][1000 genomes]
rs4698395	0.82[CEU][hapmap]
rs6810461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6836616	0.83[JPT][hapmap]
rs7675761	0.81[CEU][hapmap]
rs9993748	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998697	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15481600-15490200	Weak transcription	Esophagus	oesophagus
2	chr4:15481600-15498600	Weak transcription	Liver	Liver
3	chr4:15481600-15519000	Weak transcription	Gastric	stomach
4	chr4:15482000-15491000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:15482000-15491800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:15482200-15490400	Weak transcription	A549	lung
7	chr4:15482200-15519800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:15482600-15516600	Weak transcription	Brain Angular Gyrus	brain
9	chr4:15482600-15526400	Weak transcription	HMEC	breast
10	chr4:15482800-15518200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:15483000-15490200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:15483600-15493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:15483600-15498600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:15484800-15490000	Weak transcription	Osteobl	bone
15	chr4:15485000-15490200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:15485000-15490200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:15485000-15490200	Weak transcription	Fetal Intestine Small	intestine
18	chr4:15485000-15490200	Weak transcription	Lung	lung
19	chr4:15485000-15504800	Weak transcription	Ovary	ovary
20	chr4:15485200-15494400	Weak transcription	Fetal Heart	heart
21	chr4:15485600-15489800	Weak transcription	NHLF	lung
22	chr4:15486200-15490200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:15486200-15490200	Weak transcription	Aorta	Aorta
24	chr4:15486200-15490200	Weak transcription	Fetal Stomach	stomach
25	chr4:15486200-15490200	Weak transcription	Left Ventricle	heart
26	chr4:15486600-15490000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:15486600-15490200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:15486600-15499800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:15486800-15490200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:15486800-15490200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:15487000-15490200	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:15487200-15498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:15487400-15490000	Weak transcription	Fetal Kidney	kidney
34	chr4:15487400-15490200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
36	chr4:15487600-15489800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:15487600-15490000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:15487800-15489800	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:15487800-15490200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:15488600-15491000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:15488800-15490000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:15488800-15492200	ZNF genes & repeats	Fetal Lung	lung
43	chr4:15489600-15490200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
44	chr4:15489600-15490400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links